Reaction coordinate determination method

Initially, we have applied the modified NEB method to the calculation of both steps of the 40T catalyzed reaction. The free energy profiles and relative free energies obtained with this method were compared to our previously determined profiles [33], As we had previously shown, the calculated MEPs for Ref. [33] determined with the reaction coordinate driving method, and the MEPs for Ref. [25] calculated with the parallel path optimizer method, agree in the overall shape and relative potential energies. This provides a good starting point for our comparison. 

The SES, ESP, and NES methods are particularly well suited for use with continuum solvation models, but NES is not the only way to include nonequilibrium solvation. A method that has been very useful for enzyme kinetics with explicit solvent representations is ensemble-averaged variational transition state theory [26,27,87] (EA-VTST). In this method one divides the system into a primary subsystem and a secondary one. For an ensemble of configurations of the secondary subsystem, one calculates the MEP of the primary subsystem. Thus the reaction coordinate determined by the MEP depends on the coordinates of the secondary subsystem, and in this way the secondary subsystem participates in the reaction coordinate. 

Let us apply this method to the hypothetical reaction coordinate diagram of Fig. 5-11, which consists of two sections. The requisite energy differences are for the vertical distances (T2 — R) and (T3 — I2). Because (T3 — I2) > (T2 — R), the second section contains the rds, which must be the I2 —> T3 step. Note that T3 actually has a lower free energy than do Ti and T2 it is the change in free energy from the valley at the beginning of the section that determines the rate. 

Example 7.13 Use the reaction coordinate method to determine equilibrium concentrations for the reaction of Example 7.11. Specifically, determine the equilibrium mole fraction of component A at r= 550 K as a function of pressure, given that the reaction begins with pure A. 

One of the procedures employed for the determination of the MEP is the CD method [19], This method introduces a harmonic restraint on the reaction coordinate, which is a linear combination of the distances between the atoms involved in the reaction to perform an optimization along a proposed reaction path. In this case the reaction coordinate is given by the expression ... 

The procedure and methods for the MEP determination by the NEB and parallel path optimizer methods have been explained in detail elsewhere [25, 27], Briefly, these methods are types of chain of states methods [20, 21, 25, 26, 30, 31]. In these methods the path is represented by a discrete number of images which are optimized to the MEP simultaneously. This parallel optimization is possible since any point on the MEP is a minimum in all directions except for the reaction coordinate, and thus the energy gradient for any point is parallel to the local tangent of the reaction path. 

In the adiabatic bend approximation (ABA) for the same reaction,18 the three radial coordinates are explicitly treated while an adiabatic approximation was used for the three angles. These reduced dimensional studies are dynamically approximate in nature, but nevertheless can provide important information characterizing polyatomic reactions, and they have been reviewed extensively by Clary,19 and Bowman and Schatz.20 However, quantitative determination of reaction probabilities, cross-sections and thermal reaction rates, and their relation to the internal states of the reactants would require explicit treatment of five or the full six degrees-of-freedom in these four-atom reactions, which TI methods could not handle. Other approximate quantum approaches such as the negative imaginary potential method16,21 and mixed classical and quantum time-dependent method have also been used.22... 

To evaluate solvent effeets, statistieal meehanical Monte Carlo simulations have been carried out. An important quantity to be computed is the potential of mean force, or free energy profile, as a funetion of the reaction coordinate, X, for a chemical reaction in solution using free energy perturbation method. (44) A straightforward approaeh is to determine free energy differences for incremental changes of certain geometrieal variables that characteristically reflect the... 

The import of diabatic electronic states for dynamical treatments of conical intersecting BO potential energy surfaces is well acknowledged. This intersection is characterized by the non-existence of symmetry element determining its location in nuclear space [25]. This problem is absent in the GED approach. Because the symmetries of the cis and trans conformer are irreducible to each other, a regularization method without a correct reaction coordinate does not make sense. The slope at the (conic) intersection is well defined in the GED scheme. Observe, however, that for closed shell structures, the direct coupling of both states is zero. A configuration interaction is necessary to obtain an appropriate description in other words, correlation states such as diradical ones and the full excited BB state in the AA local minimum cannot be left out the scheme. 

R. A. Marcus It certainly is a good point that transition state theory, and hence RRKM, provides an upper bound to the reactive flux (apart from nuclear tunneling) as Wigner has noted. Steve Klippenstein [1] in recent papers has explored the question of the best reaction coordinate, e.g., in the case of a unimolecular reaction ABC — AB + C, where A, B, C can be any combination of atoms and groups, whether the BC distance is the best choice for defining the transition state, or the distance between C and the center of mass of AB, or some other combination. The best combination is the one which yields the minimum flux. In recent articles Steve Klippenstein has provided a method of determining the best (in coordinate space) transition state [1]. 

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